We booked with Alcatrazcruises.com when we went in August last year, I think that's the official site and we had no problems. I'd definitely recommend booking early as there were lots of disappointed faces at the Pier when we went, we also talked to several people during our stay who were unable to get tickets as they had left it too late to book.
Agree with PPs about booking ahead of time. When we went we pre-booked and our trip was sold out as were most of the other trips that day. There are several boat tour companies in the bay but only 1(Alcatrazcruises) went to the island. The others just went by or around. Since Alcatraz is part of the National Park system you can double check their website for the most current info
As was noted, alcatrazcruises.com (Hornblower Cruises) is the official concessionaire of the National Park Service. They are the only authorized means for private citizens to get onto the island. The audio tour is included with the transportation. All other "Alcatraz tours" either go around the island or are simply resellers of the official tour. For the most part nobody else is going to provide added value.
Another issue is parking. Parking is now free on the street on Sundays where the meters are controlled by the city/county of San Francisco, but otherwise there are pay lots. It may be confusing because the city may not have removed the tags saying that parking is charged on Sundays, and some locations are charged 7 days, like Fisherman's Wharf. The Port of San Francisco operates its own meters on the waterfront 7 days a week, so look carefully for who operates the meters. I believe one of the piers has $10 parking for those with cruise reservations. That might only be for dining cruise reservations though.
If you take public transportation, then don't worry about parking. The F-line works really well to get to the launch area for the Alcatraz boats.
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